He was re-elected in every subsequent election (representing Gander—Grand Falls after 1988) until his appointment to the Senate by Governor General Adrienne Clarkson, on the recommendation of Prime Minister Jean Chrétien, in 2002.
Although a popular and articulate MP, he was hurt by the tradition of appointing no more than one Canadian Cabinet minister from Newfoundland at a time, and by his reputation as a maverick who said what he thought rather than what the party leadership would like him to say.
Fred Mifflin's and Brian Tobin's appointments to cabinet following the 1993 election meant Baker had to remain on the backbench.
Tobin's resignation from the cabinet to become Premier of Newfoundland and Labrador opened the way for Baker to be appointed as Minister of Veterans Affairs.
In March 2009, as a Liberal Senator for Newfoundland and Labrador, he was the first among Newfoundland's federal parliamentarians to overtly call for the foundation of a new sovereigntist party, based on the Bloc Québécois, largely in response to the $1.7 billion cuts in equalization payments that represented no less than 20% of the province's budget, due to a change of how natural resources are factored in the calculation of equalization transfers.